#! /bin/bash
#! -N impute2
#$ -q 1-day
#$ -l h_vmem=5G
#$ -M prodduturi.naresh@mayo.edu
#$ -m abe
#$ -o /data4/bsi/bioinf_ext1/s112349.ucsf/newdata/MAYO/impute2_2/ 
#$ -e /data4/bsi/bioinf_ext1/s112349.ucsf/newdata/MAYO/impute2_2/
####workdir = 
#k=`cat /data4/bsi/bioinf_ext1/s112349.ucsf/newdata/MAYO/impute2_2/file_runimpute|head -$SGE_TASK_ID |tail -1`
/data4/bsi/bioinf_ext1/s112349.ucsf/newdata/UCSF/impute2_2/impute_v2.2.2_x86_64_static/impute2 $k  -m /data4/bsi/bioinf_ext1/s112349.ucsf/newdata/impute_ref/genetic_map_chr20_combined_b37.txt -h /data4/bsi/bioinf_ext1/s112349.ucsf/newdata/impute_ref/ALL_1000G_phase1integrated_feb2012_chr20_impute.hap.gz -l /data4/bsi/bioinf_ext1/s112349.ucsf/newdata/impute_ref/ALL_1000G_phase1integrated_feb2012_chr20_impute.legend.gz -g /data4/bsi/bioinf_ext1/s112349.ucsf/newdata/MAYO/impute2_2/snps_chr20.genotype -int 60270556 64387556 -o /data4/bsi/bioinf_ext1/s112349.ucsf/newdata/MAYO/impute2_2/chr20.one.phased.impute2_fil_chr20_test_extrasnps
